Variant report

Variant	rs666254
Chromosome Location	chr6:4077535-4077536
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf201-4	chr6:4076360-4079955	NONHSAT107293

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs101418	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11755877	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs1204951	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2326408	0.86[ASN][1000 genomes]
rs2473597	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2745453	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2745455	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2783063	0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2783073	0.86[ASN][1000 genomes]
rs582008	0.80[CHB][hapmap]
rs583782	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs583881	0.80[CHB][hapmap]
rs584585	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs588158	0.89[ASN][1000 genomes]
rs589494	0.87[ASN][1000 genomes]
rs590675	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs592953	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs593291	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs594662	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs595413	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs608195	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs609946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs611500	0.86[ASN][1000 genomes]
rs612022	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs612477	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs613028	0.88[ASN][1000 genomes]
rs613260	0.86[ASN][1000 genomes]
rs613709	0.86[ASN][1000 genomes]
rs617604	0.95[ASN][1000 genomes]
rs617790	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs619439	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs619483	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs619873	0.86[ASN][1000 genomes]
rs620484	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs620901	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs626080	0.84[CHB][hapmap];0.88[ASN][1000 genomes]
rs627259	0.93[ASN][1000 genomes]
rs629362	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs633290	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs634114	1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs634698	0.94[CHB][hapmap];0.86[ASN][1000 genomes]
rs634970	0.80[CHB][hapmap]
rs638329	0.80[CHB][hapmap]
rs639905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs643232	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs646385	0.81[CHB][hapmap]
rs648900	0.86[ASN][1000 genomes]
rs649725	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs650183	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs651246	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs653431	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs654621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs654982	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs659025	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs659305	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs6597028	0.93[CEU][hapmap]
rs660560	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs661404	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs661657	0.94[ASN][1000 genomes]
rs662834	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs664299	0.84[ASN][1000 genomes]
rs664635	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs664839	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs665728	1.00[CHB][hapmap];0.83[JPT][hapmap];0.96[ASN][1000 genomes]
rs665894	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs668070	0.90[ASN][1000 genomes]
rs670932	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs671364	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs674543	0.91[ASN][1000 genomes]
rs676683	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs678285	0.80[CHB][hapmap]
rs679303	0.81[CHB][hapmap]
rs682063	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs688176	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs689308	0.86[ASN][1000 genomes]
rs694903	0.93[ASN][1000 genomes]
rs707991	1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs7166	0.86[ASN][1000 genomes]
rs7744628	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs7756630	0.91[ASN][1000 genomes]
rs7757606	0.86[ASN][1000 genomes]
rs853416	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs853417	0.86[ASN][1000 genomes]
rs853418	0.82[JPT][hapmap]
rs9328220	0.86[ASN][1000 genomes]
rs9378395	0.96[ASN][1000 genomes]
rs9405219	0.95[ASN][1000 genomes]
rs942475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv462615	chr6:4052383-4096678	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv600860	chr6:4052383-4096678	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4063400-4078800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:4064000-4077600	Weak transcription	Brain Anterior Caudate	brain
3	chr6:4066800-4079600	Weak transcription	NHLF	lung
4	chr6:4067000-4082400	Weak transcription	Brain Germinal Matrix	brain
5	chr6:4073800-4077600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:4074400-4083000	Weak transcription	Pancreas	Pancrea
7	chr6:4077000-4078200	Enhancers	HepG2	liver
8	chr6:4077200-4078200	Enhancers	Adipose Nuclei	Adipose
9	chr6:4077400-4077600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:4077400-4077800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:4077400-4077800	Enhancers	Brain Hippocampus Middle	brain
12	chr6:4077400-4078000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr6:4077400-4078000	Enhancers	Brain Substantia Nigra	brain
14	chr6:4077400-4078200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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